| Summary: | Background: Salmonids are one of the most intensely studied fish, in part due to their economic and environmentalimportance, and in part due to a recent whole genome duplication in the common ancestor of salmonids. Thisduplication greatly impacts species diversification, functional specialization, and adaptation. Extensive new genomicresources have recently become available for Atlantic salmon (Salmo salar), but documentation of allelic versusduplicate reference genes remains a major uncertainty in the complete characterization of its genome and itsevolution.Results: From existing expressed sequence tag (EST) resources and three new full-length cDNA libraries, 9,057reference quality full-length gene insert clones were identified for Atlantic salmon. A further 1,365 reference full-lengthclones were annotated from 29,221 northern pike (Esox lucius) ESTs. Pairwise dN/dS comparisons within each of 408 setsof duplicated salmon genes using northern pike as a diploid out-group show asymmetric relaxation of selection onsalmon duplicates.Conclusions: 9,057 full-length reference genes were characterized in S. salar and can be used to identify alleles andgene family members. Comparisons of duplicated genes show that while purifying selection is the predominant forceacting on both duplicates, consistent with retention of functionality in both copies, some relaxation of pressure ongene duplicates can be identified. In addition, there is evidence that evolution has acted asymmetrically on paralogs,allowing one of the pair to diverge at a faster rate.
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